HMMER is used for searching sequence databases for sequence homologs,
and for making sequence alignments. It implements methods using
probabilistic models called profile hidden Markov models (profile
HMMs). HMMER is designed to detect remote homologs as sensitively as
possible, relying on the strength of its underlying probability
models.

HMMER is often used together with a profile database, such as Pfam
or many of the databases that participate in Interpro. But HMMER
can also work with query sequences, not just profiles, just like
BLAST. For example, you can search a protein query sequence against
a database with phmmer, or do an iterative search with jackhmmer.
